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- PDB-1lmb: REFINED 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR-OP... -

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Basic information

Entry
Database: PDB / ID: 1lmb
TitleREFINED 1.8 ANGSTROM CRYSTAL STRUCTURE OF THE LAMBDA REPRESSOR-OPERATOR COMPLEX
Components
  • DNA (5'-D(*AP*AP*TP*AP*CP*CP*AP*CP*TP*GP*GP*CP*GP*GP*TP*GP*A P*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3')
  • PROTEIN (LAMBDA REPRESSOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / core promoter sequence-specific DNA binding / identical protein binding
Similarity search - Function
LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) ...LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Repressor protein cI
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBeamer, L.J. / Pabo, C.O.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Refined 1.8 A crystal structure of the lambda repressor-operator complex.
Authors: Beamer, L.J. / Pabo, C.O.
#1: Journal: Science / Year: 1991
Title: The DNA Binding Arm of a Lambda Repressor: Critical Contacts from a Flexible Region
Authors: Clarke, N.D. / Beamer, L.J. / Goldberg, H.R. / Berkower, C. / Pabo, C.O.
#2: Journal: Science / Year: 1990
Title: Conserved Residues Make Similar Contacts in Two Repressor-Operator Complexes
Authors: Pabo, C.O. / Aggarwal, A.K. / Jordan, S.R. / Beamer, L.J. / Obeysekare, U.R. / Harrison, S.C.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: Comparison of the Structures of Cro and Lambda Repressor Proteins from Bacteriophage Lambda
Authors: Ohlendorf, D.H. / Anderson, W.F. / Lewis, M. / Pabo, C.O. / Matthews, B.W.
#4: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1983
Title: Structure of the Operator-Binding Domain of Bacteriophage Lambda Repressor. Implications for DNA Recognition and Gene Regulation
Authors: Lewis, M. / Jeffrey, A. / Wang, J. / Ladner, R. / Ptashne, M. / Pabo, C.O.
#5: Journal: Nature / Year: 1982
Title: Homology Among DNA-Binding Proteins Suggests Use of a Conserved Super-Secondary Structure
Authors: Sauer, R.T. / Yocum, R.R. / Doolittle, R.F. / Lewis, M. / Pabo, C.O.
#6: Journal: Nature / Year: 1982
Title: The Operator-Binding Domain of Lambda Repressor. Structure and DNA Recognition
Authors: Pabo, C.O. / Lewis, M.
#7: Journal: Nature / Year: 1982
Title: The N-Terminal Arms of Lambda Repressor Wrap Around the Operator DNA
Authors: Pabo, C.O. / Krovatin, W. / Jeffrey, A. / Sauer, R.T.
History
DepositionNov 5, 1991Deposition site: BNL / Processing site: BNL
Revision 1.0Nov 5, 1991Provider: repository / Type: Initial release
SupersessionOct 15, 1993ID: 1LRD
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: DNA (5'-D(*AP*AP*TP*AP*CP*CP*AP*CP*TP*GP*GP*CP*GP*GP*TP*GP*A P*TP*AP*T)-3')
2: DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3')
3: PROTEIN (LAMBDA REPRESSOR)
4: PROTEIN (LAMBDA REPRESSOR)


Theoretical massNumber of molelcules
Total (without water)32,5404
Polymers32,5404
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.220, 68.720, 57.030
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*AP*AP*TP*AP*CP*CP*AP*CP*TP*GP*GP*CP*GP*GP*TP*GP*A P*TP*AP*T)-3')


Mass: 6158.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3')


Mass: 6108.967 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (LAMBDA REPRESSOR)


Mass: 10136.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / References: UniProt: P03034
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 40011
3BIS-TRIS-PROPANE_HCL11
4WATER12
5PEG 40012
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: taken from Jordan, S.R. et al.(1985). Science, 230, 1383-1385.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(v/v)PEG4001drop
220 %(v/v)PEG4001reservoir
31
41
51

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Data collection

DiffractionMean temperature: 258 K
DetectorType: UCSD MARK II / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 28193 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. measured all: 101275 / Rmerge(I) obs: 0.052

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Processing

Software
NameClassification
X-PLORrefinement
TNTrefinement
RefinementResolution: 1.8→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.189 -
obs0.189 25252
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 814 0 140 2334
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 25252 / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.2 Å2

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